title: 2173-STC1_D

treatment_protocol:
Melanoma tumors were obtained from the Melcore tumor bank at MD Anderson Cancer Center.
Tissue was disassociated (50 mg of tissue; ~8 mg per histone modification antibody) manually in 2 mL of Hanks' Balanced Salt Solution (HBSS) using a sterile razor blade. Mince the tissue into 3 to 4 mm pieces for approximately 5 min in a sterile tissue culture dish. Transfer the tissue and HBSS solution into a dissociator tube and add another 8 mL of HBSS. Further disassociate the tissue using a dissociator until homogenized. For melanoma tumors, place the tubes in a dissociator and run the following cycles each one time in this order: h_tumor_01.01, h_tumor_02.01, h_tumor_03.01 and m_heart_02.01.

value: Cell Line

value: H3K79me2 Abcam ab3594


title: 4cell_siZcchc8_2

status: Public on Nov 07 2019

type: SRA

city: shanghai

first: You

last: Wu

address: 1239 siping road

department: school of life science and technology

country: China

institute: tongji university

library_source: transcriptomic

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v2.1.1 with default parameters.
Gene expression for each sample was quantified to FPKM using Cufflinks(v 2.2.1).
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include FPKM values for each transcript.

molecule: total RNA

organism: Mus musculus

source_name: siZcchc8_four cell stage embryos

extract_protocol:
2-5embryos were collected as one replicate. Zona pellucida of embryos were removed with 0.5% protease E (Sigma). Embryos were washed for 5-6 times in 0.5% BSA(Sigma) in PBS solution before put into cell lysis buffer. After incubation at 70°C for 90 seconds, reverse transcription for the first strand cDNA was performed subsequently with a 24 oligo (dT) primer. After second strand cDNA synthesis, cDNA library was amplified for 16-18 cycles based on the embryo number. Amplified cDNA was diluted for 10 times for qPCR reaction.
For library construction, amplified cDNA was sheered to 200-300 bp using Covaris S220 system. The sequence libraries were generated using KAPA HyperPlus Library Preparation kit (Roche, KK8510), following the manufacturer’s instructions. 8-12 cycles amplification was used depending on cDNA concentration.

tag: strain

tag: cell type

value: four cell stage embryos

tag: genotype/variation


title: Mcm4MYC_ChIP_tof1D_AS

city: Geneva

first: Maksym

last: Shyian

state: Geneva

address: 30 quai Ernest-Ansermet, CH-1211, Geneva 4, Switzerland

department: Molecular Biology

country: Switzerland

institute: University of Geneva

library_source: genomic

data_processing:
For ChIP-Seq raw reads were aligned to the sacCer3  genome assembly using Bowtie2 with options "-k 20 --end-to-end --sensitive -X 800".
For ChIP-Seq, data were filtered to retain only the mapped reads with at most 5 hits in the reference.
For ChIP-Seq, the reads were shifted by 100 bp and extended by 50 bp
Genome_build: sacCer3
Supplementary_files_format_and_content: wig and bigwig files were obtained using HTSStation (http://htsstation.epfl.ch)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: whole organism

growth_protocol: Asyncrhonous cell culture

extract_protocol:
anti-MYC (Top1-MYC, noMYC, Mcm4-MYC, Cdc45-MYC, Pol2-MYC) ChIP-seq was performed as described previously (Ribaud et al., 2012) (PMID: 21952045)
TruSeq ChIP library preparation kit (Illumina)

treatment_protocol: no treatment

tag: genotype

value: W303 MATa RAD5+ bar1D Mcm4-13MYC::HIS3MX4 tof1D::LEU2

tag: antibody

value: Anti-MYC


title: blastocyst_control_2

source_name: wild type_blastocyst stage embryos

value: blastocyst stage embryos

value: wild type


title: input DNA_CS_2212_003

city: Shinjuku

first: Kenta

last: Masui

state: Tokyo

address: 8-1 Kawada-cho

department: Department of Pathology

country: Japan

institute: Tokyo Women's Medical University

data_processing:
The Illumina Hiseq generates raw images utilizing HCS (HiSeq Control Software v2.2) for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis. v1.18). The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq (v1.8.4).
Adapter and low-quality sequences were removed by cutadapt (v1.2.1).
The trimmed reads were aligned to the reference human genome (hg19) using BWA (ver.0.6.2). After that, the reads whose Mapping Quality were zero were removed.
The peaks were called using MACS (ver.1.4.2) with default setting.
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated by MACS and wig files were converted to bigwig files using wigToBigWig (v 4). Scores represent the pileup of reads (10 bp resolution).

organism: Homo sapiens

source_name: Glioblastoma cells

growth_protocol: U87-EGFRvIII GBM cell lines were cultured in DMEM supplemented with 10% FBS (Omega Scientific, Tarzana, CA) in a humidified 5% CO2 incubator at 37°C.

extract_protocol:
Lysates were prepared with SimpleChIPTM Enzymatic Chromatin IP Kit (CST, Beverly, MA) and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to instructions accompanying the KAPA library preparation kit.

treatment_protocol: U87-EGFRvIII cells were treated with siRNA against Scramble sequence or Rictor (Santa Cruz, Dallas, TX) for 48 hours.

tag: cell line

value: glioblastoma cells

tag: RNAi treatment

value: Scramble

tag: chip antibody


title: 08_0537_Parental

type: genomic

city: Durham

first: Hai

last: Yan

state: NC

address: 199B-MSRB, Research Drive

department: Pathology

country: USA

institute: Duke University

hyb_protocol: Followed the manufacturer's (Illumina) specifications.

scan_protocol: Followed the manufacturer's (Illumina) specifications on an iScan.

data_processing: Data were interpreted in GenomeStudio v2011.1 Methylation Module 1.9.0 and exported for analysis or were processed in R using ChAMP v. 2.12.4 packages.

label: biotin nucleotide or dinitrophenyl labeled

label_protocol: A single nucleotide extension was labeled either with biotin or dinitrophenyl according to the manufacturer's (Illumina) specifications.

extract_protocol: Genomic DNA was extracted using Qiagen All Prep RNA/DNA kit and passed through a Zymo genomic DNA Clean and concentrator kit. Extracted DNA was bisulfite treated with the Zymo bisulfite kit according the manufacturer's specifications.

treatment_protocol: Electroporation of Cas9 for transient expression, flow sorting and single cell dilution.

value: glioma cells

tag: idh1 status


title: IMA_Clone4_Replicate1


title: Mcm4MYC_ChIP_WT_AS

value: W303 MATa RAD5+ bar1D Mcm4-13MYC::HIS3MX4


title: H3K9ac_ChIPSeq_CS_2212_002

value: Rictor

value: Acetyl-Histone H3 (Lys9) (C5B11) (CST, Rabbit mAb #9649)


title: 4cell_control_3

source_name: wild type_four cell stage embryos


title: 4cell_control_2


title: noMYC_ChIP_rrm3D_AS

description: anti-MYC ChIP negative control (strian without MYC-tagged proteins)

value: W303 MATa RAD5+ bar1D Mcm4-3FLAG::KANMX rrm3D::HPHMX4


title: 4cell_control_1


title: H1047R-3

city: La Jolla

first: Jonathan

middle: Ross

last: Hart

state: CA

address: 10550 North Torrey Pines Road, BCC239

department: Molecular and Experimental Medicine

institute: The Scripps Research Institute

data_processing:
Basecalling with Cassava 1.8
Alignment to genome using RNA STAR 2.6.0b.  Exact parameters are STAR --genomeDir ${genome} --readFilesIn $fq1 \      --readFilesCommand zcat --runThreadN 12 --genomeLoad NoSharedMemory \      --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 \      --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.04 \      --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 \      --outSAMunmapped Within --outFilterType BySJout \      --outSAMattributes NH HI AS NM MD \      --outSAMtype BAM Unsorted \      --quantMode TranscriptomeSAM GeneCounts \      --outFileNamePrefix $prefix --outTmpDir $scratch/star
Sorted alignments using Sambamba v0.5.4 Exact command line: sambamba sort -t 12 -m 26G --tmpdir=$scratch -l 9 -o $outBam $inBam
Counted alignments with HTSEQ-count v0.9.1 Exact command line: htseq-count -f bam -r pos --max-reads-in-buffer 100000000 -s yes $array > $out
Genome_build: hg38.d1.vd1
Supplementary_files_format_and_content: Raw counts of alignments to Gencode version 27

source_name: breast epithelial cells

growth_protocol: 500k Cells were seeded in 10cm petri dishes in DMEM/F12 growth medium. After 24 hours, medium was changed to MCDB-170 serum free media. Cells were allowed to grow an additional 24 hours. Medium was changed once more and cells harvested at 6 hours post medium exchange.

extract_protocol:
Cells were then harvested by suspending them with trypsin and neutralized with soybean trypsin inhibitor (ThermoFisher), and total RNA isolated using the Maxwell RSC simplyRNA cells kit (Promega), as per the manufacturer’s instructions.
Total RNA was ribosome depleted and libraries were constructed by Genewiz following Illumina protocols.

treatment_protocol: No drug treatment

tag: kras status

value: WT

tag: pik3ca  status

value: breast epithelial cells


title: mESCs_differentiation_MeOH 24h_rep2

type: RNA

city: Kiel

first: Dennis

last: Schade

address: Gutenbergstr. 76

department: Pharmaceutical and Medicinal Chemistry

country: Germany

institute: Christian-Albrechts-University Kiel

description: gene expression after 24h treatment with MeOH eluate (0.1 mg/mL)

hyb_protocol: For hybridisation, the Agilent Gene Expression Hybridisation Kit (Agilent Technologies) is used. For example, 600 ng of each cRNA is hybridised on 8x60K microarrays at 65°C for 17 h using Agilent's recommended hybridisation chamber and oven. Afterwards microarrays are washed once with the Agilent Gene Expression Wash Buffer 1 for one minute at ambient temperature followed by a second wash with preheated (37°C) Gene Expression Wash Buffer 2 for one minute.

scan_protocol: Fluorescence signals on microarrays are detected by the SureScan Microarray Scanner (Agilent Technologies) at a resolution of 3 micron for SurePrint G3 Gene Expression Microarrays and 5 micron for HD Microarray formats, generating a 20 bit TIFF file

data_processing: Data of all samples were quantile normalized using the ranked mean quantiles according to Bolstad et al. (2003).

source_name: mESC_MeOH 24h_replicate 2

label_protocol: For genome-wide gene expression analysis on OakLabs' ArrayXS Agilent microarrays as well as on Agilent's catalogue microarrays, OakLabs fulfills the requirements for certified service providers and follows strictly the relevant protocols. For labelling, the Low Input QuickAmp Labeling Kit (Agilent Technologies) is used to generate fluorescent cRNA (complementary RNA). For 1st strand synthesis, either oligo-dT primer or a random primer / oligo-dT primer mixture (WT primer) is used. After 2nd strand synthesis, an in vitro transcription for synthesis of cRNA labelled with cyanine 3-CTP is performed. Please refer the „characteristics column“ in the Metadata file for details regarding RNA integrity number (RIN), yield of cRNA as well as Cy3 incorporation rate.

growth_protocol: CGR8-Myh6-GFP mESCs were grown under feeder-free conditions as monolayers and maintained in DMEM (Gibco®) supplemented with 10% fetal bovine serum (FBS, PAN Biotech), 1% L glutamine (Gibco®), 1% non-essential amino acids (Gibco®), 1% penicillin/streptomycin (Gibco®), 0.1 mM 2 mercaptoethanol (Gibco®), and 15 ng/mL murine LIF (Dortmund Protein Facility). Cells were cultured on 0.1% gelatine-coated 6-well plates (at 37°C, 5% CO2) and passaged after 2-3 days when confluency reached 60-70% to preserve the undifferentiated phenotype. For mESC cardiac differentiation, cells were trypsinized and cultured in differentiation media (at 37°C, 5% CO2) on 0.1% gelatine-coated 384 well plates at a density of 500 cells per 50 µL differentiation media per well (= d0). The differentiation media was composed of DMEM (Gibco®) supplemented with 10% FBS (PAN Biotech), 1% L glutamine (Gibco®), 1% non-essential amino acids (Gibco®), 1% penicillin/streptomycin (Gibco®), and 0.1 mM 2-mercaptoethanol (Gibco®). At day 3 of differentiation (= d3), media was added to 75 µL assay volume. Treatments started on day 4 of differentiation (see below)

extract_protocol: RNA extraction was performed by OakLabs (Hennigsdorf, Germany). Briefly, quality control of RNA samples was accomplished with the 2100 Bioanalyzer (Agilent Technologies) using the RNA 6000 Pico Kit. For quantity control, a photometrical measurement with the Nanodrop 2000 spectrophotometer (Thermo Scientific) was performed.

treatment_protocol: Cells were treated with extract WS1442 or MeOH eluate or DMSO on day 4 of differentiation for either 6h or 24h, before cells were harvested for RNA isolationa nd transcriptome analysis. As a control of the experiment (successful cardiac differentiation), each treatment condition was in at least 8 wells continued until day 6, followed by media changes every 48h. On day 11 of differentiation (= d11) cells were fixed in 4% paraformaldehyde and incubated with DAPI for nucleic acid staining. Myh6-GFP positive cells were imaged on a MicroXL System (Molecular Devices) and GFP levels from images were quantified with MetaXpress Software, using a multi-wavelength scoring algorithm (Molecular Devices).

tag: rin

tag: crna yield (microg)

tag: cy3 incorporation (pmol/microg)

tag: time point

value: after 24h treatment

tag: agent

value: MeOH eluate (0.1 mg/mL)


title: mESCs_differentiation_MeOH 24h_rep1

source_name: mESC_MeOH 24h_replicate 1


title: noMYC_ChIP_WT_AS

value: W303 MATa RAD5+ bar1D Mcm4-3FLAG::KANMX


title: totalRNA_KO_2_8h

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm9 reference genome using tophat v2.1.1 with default parameters.
For RNA half-life test, gene and ERCC reads count were calculated using Htseq-count (v 0.6.0).
Gene counts were normalized by ERCC normalizing factor which got from estimateSizeFactorsForMatrix for ERCC counts using DESeq2 tools.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text files include ERCC normalized counts at different treated time were assembled in text files.

growth_protocol: ESC derived from blastocysts (BDF1 strain) were cultured in ESC medium: DMEM (Gibco),15% fetal bovine serum (Hyclone), nucleosides (100×),1 mM l-glutamine,1% nonessential amino acid stock, 0.1 mM mercaptoethanol, 1,000 U/ml LIF (Merk Millipore), 3 m CHIR99021 (S2924; Selleck) and 1 M PD0325901 (S1036; Selleck).

extract_protocol:
Total RNA was obtained from at least 5×10^5 ESCs via RNeasy Mini Kit extraction(Qiagen).
For total RNA (rRNA erased), 1μg total RNA were used for RNA-seq with the KAPA RiboErase Kit (Roche) following the manufacturer’s instructions.

treatment_protocol: ESCs were treated with Actinomycin D at 5μg/ml final concentration.

value: derived ESC

value: Zcchc8 KO

tag: treatment

value: Actinomycin D treatment for 8h. ERCC spike-in added.


title: H3K9ac_ChIPSeq_CS_2212_001


title: Top1_ChIP_tof1D_earlyS-b

description: biological replicate 2 (-b)

growth_protocol: Synchronous release into S phase, ealy S phase time point (45min at 18C)

treatment_protocol: alpha-Factor for 2.5 hrs and then release with pronase

tag: strain

value: W303 MATa RAD5+ bar1D Mcm4-3FLAG::KANMX TOP1-13MYC::HIS3MX4 tof1D::LEU2

value: Anti-MYC


title: 4cell_siZcchc8_1

tag: cell type

value: four cell stage embryos


title: mESCs_differentiation_MeOH 24h_rep3

source_name: mESC_MeOH 24h_replicate 3


title: H1047R-2


title: Top1_ChIP_tof1D_earlyS-a

description: biological replicate 1 (-a)


title: totalRNA_KO_1_8h

tag: genotype/variation


title: mESCs_differentiation_WS1442 24h_rep3

description: gene expression after 24h treatment with WS1442 (0.25 mg/mL)

source_name: mESC_WS1442 24h_replicate 3


title: Top1_ChIP_WT_earlyS-b

description: biological replicate 2 (-b)

tag: genotype

value: W303 MATa RAD5+ bar1D Mcm4-3FLAG::KANMX TOP1-13MYC::HIS3MX4


title: pan_28

city: Vienna

first: Tibor

last: Harkany

address: Spitalgasse 4

department: Department of Molecular Neurosciences (Center for Brain Research)

country: Austria

institute: Medical University of Vienna

data_processing:
Raw fastq files were processed within the NextFlow methylseq pipeline (Dockerfile v.1.3) with --aligner bismark --singleEnd --genome mm10 –rrbs parameters to obtain methylation coverage7°
RnBeads (Muller et al, 2019) were used for quality control and initial analysis of the DNA methylation data according to established practices (Bock, 2012).
We summarized CpGs in 1,000 kb bins and performed differential DNA methylation analysis between amphetamine treatment (n = 5) vs. control (n = 6) or male (n = 5) vs. female (n = 6) datasets using limma (Ritchie et al, 2015) (FDR-adjusted p-value < 0.05, f
The relative over-representation of hypermethylated and hypomethylated tiles was used for GO pathway enrichment analysis (Falcon et al, 2007).
Additionally, we performed base-pair level and region level (for promoters) analysis using methylKit (Akalin et al, 2012)on Bismark methylation call output files. We used both Fisher’s exact test on pooled samples and the chisqr-test with overdispersion f
Genome_build: mm10
Supplementary_files_format_and_content: Methylation signal in bigWig file format

growth_protocol: Each litter was kept equal in size until weaning. Animals were kept in groups of 6 under standard housing conditions with a 12 h/12 h light/dark cycle and food and water available ad libitum. Experiments on live animals conformed to the 2010/63/EU Europea

extract_protocol:
Pancreas samples were homogenized by using a TissueLyser II (Qiagen) with the following settings: 4 x 30sec, 30Hz with RNAse/DNAse-free ceramic beads. Tissues were dissolved in RLT lysis buffer of the DNA/RNA Allprep Kit (Qiagen) following the manufacture
Extracted DNA was subjected to the reduced representation bisulfite sequencing (RRBS) workflow as described previously (Klughammer et al, 2018). One hundred ng of DNA were digested at 37°C for 12 h with 20 units of MspI and TaqI (New England Biolabs) in e

treatment_protocol: On embryonic days (E) 14.5, 15.5 and 16.5, pregnant C57BL/6N mice (Charles River) were injected with amphetamine (n > 10; 10 mg/kg body weight). Offsprings were analyzed after daily in utero exposure to amphetamine. On P0, offspring in each litter was ran

value: wild type

tag: Sex

value: male

value: Amphetamine

tag: tissue

value: Pancreas


title: WT-2

tag: cell line


title: totalRNA_KO_2_4h

value: Actinomycin D treatment for 4h. ERCC spike-in added.


title: pan_02

value: Saline


title: Top1_ChIP_WT_earlyS-a

description: biological replicate 1 (-a)

tag: antibody


title: WT-1

value: WT

value: breast epithelial cells


title: totalRNA_KO_1_4h


title: yap1_biological replicate 3

city: Seoul

first: Kyung-Tae

last: Lee

address: Yonsei-ro 50, Seodaemun-gu

department: Biotechnology

country: South Korea

institute: Yonsei University

data_processing:
The sequenced reads were trimmed to remove the adaptor sequence and masked for low-complexity or low-quality sequence by using Cutadapt v2.4 with Python 3.5.2 with adapter sequence i7: agatcggaagagcacacgtctgaactccagtcac and i5: agatcggaagagcgtcgtgtagggaaagagtgt.
The reads were aligned to the genome sequence of Cryptococcus neoformans var. grubii H99 strain retrieved from the Broad Institute (https://www.broadinstitute.org/fungal-genome-initiative/cryptococcus-neoformans-serotype-genome-project) using Hisat2 v2.1.0 with the Hisat, and Bowtie2 algorithm [Kim 2015 Nat Methods] and processed as previously reported [Pertea 2016 Nat Protoc]. Briefly, Hisat2 was performed with “-p 30” and “--dta -1” option and other parameters set as default. Aligned reads were converted and sorted using Samtools v0.1.19 with “-Sb -@ 8” for converting, and “-@ 20 –m 2000000000” option for sorting and other parameters set as default. Transcript assembly and abundance estimation were performed by Stringtie v1.3.6 by using “-p 12” option, and also “-B” option to run the Ballgown. Assembled transcripts were merged to single GTF file, and the relative transcript abundances were displayed via FPKM (Fragments Per Kilobase of exon per Million fragments mapped).
Genome_build: Cryptococcus neoformans var. grubii H99 strain retrieved from the Broad Institute (https://www.broadinstitute.org/fungal-genome-initiative/cryptococcus-neoformans-serotype-genome-project)
Supplementary_files_format_and_content: Tab-delimited text files include FPKM and expected counts for each Sample.

molecule: polyA RNA

organism: Cryptococcus neoformans H99

source_name: yap1∆ mutant (YSB815) _YPD

growth_protocol: WT (H99) and yap1∆ mutant (YSB815) strains were incubated in liquid YPD medium overnight at 30°C. The cells were subcultured in fresh YPD medium and then further incubated at 30°C until OD600 reached 0.8) .

extract_protocol:
The WT and yap1∆ mutant cells were harvested and lyophilized. Three biologically independent cultures were prepared for each strain. Total RNAs were isolated by Easy-BLUE (iNtRON) and purified with an RNeasy Mini Kit (Qiagen).
cDNA libraries were constructed with the TruSeq RNA library kit v2 (Illumina) using 1ug of total RNA.

treatment_protocol: Basal condition in liquid YPD medium

value: yap1 mutant

tag: growth medium

value: YPD

tag: growth phase


title: H1047R-1

tag: kras status

tag: pik3ca  status


title: totalRNA_KO_2_0h

value: derived ESC

value: Actinomycin D treatment for 0h. ERCC spike-in added.


title: mESCs_differentiation_WS1442 24h_rep2

source_name: mESC_WS1442 24h_replicate 2

tag: rin

tag: crna yield (microg)

value: after 24h treatment


title: mESCs_differentiation_WS1442 24h_rep1

source_name: mESC_WS1442 24h_replicate 1

tag: cy3 incorporation (pmol/microg)

tag: time point


title: totalRNA_KO_1_0h

value: Zcchc8 KO

tag: treatment


title: mESCs_differentiation_MeOH 6h_rep3

description: gene expression after 6h treatment with MeOH eluate (0.1 mg/mL)

source_name: mESC_MeOH 6h_replicate 3

value: after 6h treatment

tag: agent

value: MeOH eluate (0.1 mg/mL)


title: yap1_biological replicate 2


title: mESCs_differentiation_MeOH 6h_rep2

source_name: mESC_MeOH 6h_replicate 2


title: totalRNA_C_2_8h

tag: strain

tag: cell type

value: Actinomycin D treatment for 8h. ERCC spike-in added.


title: yap1_biological replicate 1

tag: genotype/variation


title: WT_biological replicate 3

source_name: WT (H99)_YPD

value: wild type


title: AL (Apis laboriosa) transcriptome

city: Beijing

first: long

last: su

state: Beijing

address: Xiangshan Street

institute: sulong

data_processing:
Firstly, raw reads were processed and filtered by removing reads with sequencing adaptors, reads with low quality (quality scores < 20) and reads containing unknown nucleotides to get clean reads. All downstream analyses were based on those clean reads.
Next, transcriptome de novo assembly was performed by using Trinity software, with min_kmer_cov set to 2 and all other parameters set default. Only contigs longer than 200 bp were retained.
Then, the transcriptome obtained by splicing with Trinity was used as a reference sequence (ref), and we use RSEM software to map the clean reads of each sample to reference, and the number of readcounts aligned to each gene was further obtained. We use the most commonly method for estimating gene expression is that take readcount number for FPKM conversion
Finally, CD-HIT-EST program was used to parse the transcripts obtained from Trinity software, with a sequence identity threshold of 0.99 and other parameters as default, to only keep the longest transcript of each gene (unigene) for downstream analysis.
Supplementary_files_format_and_content: Fasta files include protein-coding sequences; txt files include FPKMs for protein-coding sequences

organism: Apis laboriosa

source_name: giant Himalayan honeybee

extract_protocol:
For each species, total RNA was isolated from each of the three samples, respectively, using the TRIzol reagent (Invitrogen, CA, USA). After quantifying the concentration of obtained RNA by Qubit® 2.0 Flurometer (Life Technologies, CA, USA), a single pooled RNA sample was prepared for each species by mixing equal amount of the RNA (1 μg) extracted from each of the three samples.
The pooled 3 μg of RNA sample was used as input material for the species to construct sequencing libraries, which were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

tag: number

tag: altitude

value: whole body without belly


title: AD (Apis dorsata) transcriptome

organism: Apis dorsata

source_name: giant honeybee

tag: tissue


title: WT_biological replicate 2


title: 2173-STC1_G

city: Houston

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

data_processing:
Raw fastq reads for all ChIP-seq experiments were processed using a snakemake based pipeline54. Briefly, raw reads were first processed using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and uniquely mapped reads were aligned to the hg19 reference genome using Bowtie version 1.1.2. Duplicate reads were removed using SAMBLASTER before compression to bam files. To directly compare ChIP-seq samples uniquely mapped reads for each mark were downsampled per condition to 18 million, sorted and indexed using samtools version 1.5. To visualize ChIP-seq libraries on the IGV genome browser, we used deepTools version 2.4.0  to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM). Super ChIP-seq tracks were generated by merging bam files from each cancer type, sorting and indexing using samtools and scaling to RPKM using deepTools.
Genome_build: hg19
Supplementary_files_format_and_content: Model based analysis of ChIP-seq (MACS) version 1.4.2 peak calling algorithm with a p-value threshold of 1e-5 to identify H3K4me3, H3K27ac and H3K4me1 and MACS version 2.1 p-value threshold of 1e-5 were used to idenftify H3K27me3, H3K9me3 and H3K79me2 enrichment over “input” background
Supplementary_files_format_and_content: deepTools version 1.5 was used to generate bigWig files by scaling the bam files to reads per kilobase per million (RPKM).

source_name: Melanoma Short Term Cultures

extract_protocol:
ChIP assays were performed as described previously in Terranova et al (An Integrated Platform for Genome-wide Mapping of Chromatin States Using High-throughput ChIP-sequencing in Tumor Tissues; JoVE 2018). Briefly, 50mg of tissue or 20million cells were harvested via cross-linking with 1% (wt/ vol) formaldehyde for 10 min at 37 °C with shaking. After quenching with 150 mM glycine for 10 min at 37 °C with shaking, cells were washed twice with ice-cold PBS and frozen at −80 °C for further processing. Cross-linked pellets were thawed and lysed on ice for 30 min in ChIP harvest buffer (12 mM Tris-Cl, 1 × PBS, 6 mM EDTA, 0.5% SDS) with protease inhibitors (Sigma). Lysed cells were sonicated with a Bioruptor (Diagenode) to obtain chromatin fragments (~200–500 bp) and centrifuged at 15,000 × g for 15 min to obtain a soluble chromatin fraction. In parallel with cellular lysis and sonication, antibodies (5 μg/3 × 106 cells) were coupled with 30 μl of magnetic protein G beads in binding/blocking buffer (PBS + 0.1% Tween + 0.2% BSA) for 2 h at 4 °C with rotation. Soluble chromatin was diluted five times using ChIP dilution buffer (10 mM Tris-Cl, 140 mM NaCl, 0.1% DOC, 1% Triton X, 1 mM EDTA) with protease inhibitors and added to the antibody-coupled beads with rotation at 4 °C overnight. After washing, samples were treated with elution buffer (10 mM Tris-Cl, pH 8.0, 5 mM EDTA, 300 mM NaCl, 0.5% SDS), RNase A, and Proteinase K, and cross-links were reversed overnight at 37. Immune complexes were then washed five times with cold RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 140mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), twice with cold high-salt RIPA buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 500mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC), and twice with cold LiCl buffer (10mM Tris–HCl, pH 8.0, 1mM EDTA, pH 8.0, 250mM LiCl, 0.5% NP-40, 0.5% DOC).  ChIP DNA was purified using AMPure XP beads (Agencourt) and quantified using the Qubit 2000 (Invitrogen) and Bioanalyzer 1000 (Agilent). Libraries for Illumina sequencing were generated following the New England BioLabs (NEB) Next Ultra DNA Library Prep Kit protocol. A total of 10 cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments (~200–500 bp) and quantified using the Qubit 2000 and Bioanalyzer 1000 before multiplexing.
Libraries for Illumina sequencing were generated following the New England BioLabs NEBNext Ultra DNA Library Prep Kit protocol. A total of 10x cycles were used during PCR amplification for the generation of all ChIP-seq libraries. Amplified ChIP DNA was purified using double-sided AMPure XP to retain fragments ~200 to 500bp and quantified using the Qubit 2000 and TapeStation 2000 before multiplexing.

value: Cell Line


title: totalRNA_C_2_4h


title: mESCs_differentiation_control 24h_rep1

description: gene expression after 24h treatment with vehicle control (DMSO)

source_name: mESC_control 24h_replicate 1

value: vehicle control (DMSO)


title: WT_biological replicate 1


title: RNA seq species 7

city: University of Helsinki

first: Nicolas

last: Di-Poi

address: Viikinkaari 1

department: Institute of Biotechnology, Helsinki Institute of Life Sciences

country: Finland

institute: University of Helsinki

data_processing:
Quality trimming and adapter sequence removal of reads were done using the Trimmomatic tool, and the SortMeRNA pipeline was used for ribosomal RNA (rRNA) filtering.
Quality trimmed and rRNA-filtered reads were de novo assembled in contigs with the Trinity software v2.8.5, using its default parameters.
The coding (CDS) and protein sequence of unigenes were then predicted using the TransDecoder program implemented in Trinity software.
The OrthoFinder algorithm was used for inferring orthologous and species-specific unigenes from protein sequences.
The relative abundance of transcripts were evaluated for each species as FPKM using the RNA-Seq by Expectation Maximization (RSEM) software.
Supplementary_files_format_and_content: Excel file including FPKM values for each squamate species.

organism: Pogona vitticeps

source_name: Cerebellum

extract_protocol:
Cerebella were dissected, flash frozen in liquid nitrogen, and RNA was harvested using the RNeasy Plus Micro Kit (Qiagen, Germany). RNA Integrity Number (RIN) values were determined using Agilent 2100 Bioanalyzer (Agilent Technologies, U.S.A.).
Libraries were produced using the TruSeq Stranded Total RNA Kit with Ribo-Zero (Human/Mouse/Rat; Illumina, U.S.A.).

value: Cerebellum

tag: age

value: Adult

tag: genotype

value: Wild-type


title: RNA seq species 8

organism: Pseudopus apodus


title: mESCs_differentiation_MeOH 6h_rep1

source_name: mESC_MeOH 6h_replicate 1


title: totalRNA_C_1_4h

value: Actinomycin D treatment for 4h. ERCC spike-in added.


title: RNA seq species 9

organism: Python regius


title: RNA seq species 6

organism: Pantherophis guttatus


title: RNA seq species 10

organism: Trioceros jacksonii


title: Skin_Sdr9c7_WT_P0

city: Tokyo

first: Tetsuya

last: Hirabayashi

address: 2-1-6 Kamikitazawa, Setagaya-ku

institute: Tokyo Metropolitan Institute of Medical Science

description:
SDR9C7_001
Gene expression in WT skins at P0

hyb_protocol: According to the Agilent Gene Expression Hybridization Kit protocol, 1.65 µg of Cy3-labeled cRNA was fragmented and hybridized on an Agilent Mouse GE 4x44K v2 Microarray for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: Slides were scanned with SureScan Microarray Scanner (Agilent Technologies) using a scan resolution of 5 µm and dye channel of Green with PMT set to 100%.

data_processing: Data was obtained using the Agilent Feature Extraction software (v11.5.1.1) with set to default for all parameters.

source_name: WT skin at P0

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit  (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: Dorsal skin was dissected from P0 newborn mice.

extract_protocol: Total RNA extracted from P0 newborns was purified using a RNeasy Mini Kit (QIAGEN). The quality of RNA was assessed with a 2100 Bioanalyzer (Agilent Technologies).

tag: strain background

value: Skin


title: mESCs_differentiation_WS1442 6h_rep3

description: gene expression after 6h treatment with WS1442 (0.25 mg/mL)

source_name: mESC_WS1442 6h_replicate 3


title: mESCs_differentiation_WS1442 6h_rep2

source_name: mESC_WS1442 6h_replicate 2


title: totalRNA_C_1_8h


title: mESCs_differentiation_WS1442 6h_rep1

source_name: mESC_WS1442 6h_replicate 1


title: Skin_Sdr9c7_KO_P0

description:
SDR9C7_002
Gene expression in KO skins at P0

source_name: KO skin at P0

value: Sdr9c7-/- (knockout)


title: totalRNA_C_2_0h

value: derived ESC


title: RNA seq species 4

organism: Eryx colubrinus


title: WT-4cell-1

source_name: four cell stage embryos

value: four cell stage embryos


title: RNA seq species 5

organism: Mochlus fernandi


title: totalRNA_C_1_0h

value: Actinomycin D treatment for 0h. ERCC spike-in added.


title: RNA seq species 3

organism: Dasypeltis gansi


title: RNA seq species 1

organism: Basiliscus vittatus


title: mESCs_differentiation_control 6h_rep2

description: gene expression after 6h treatment with vehicle control (DMSO)

source_name: mESC_control 6h_replicate 2


title: mESCs_differentiation_control 24h_rep2

source_name: mESC_control 24h_replicate 2

value: after 24h treatment


title: DoxTam_rep2

status: Public on Nov 06 2019

city: Oslo

first: Shixiong

last: Wang

address: Gaustadalléen 21

department: Centre for Molecular Medicine Norway

country: Norway

institute: University of Oslo

description:
analyzeRepeat_PAX2_gene_expression_raw_counts.txt
analyzeRepeat_PAX2_gene_expression_fpkm.txt
analyzeRepeats_PAX2_intergenic_noadj_raw_counts.txt
analyzeRepeats_PAX2_intergenic_fpkm.txt
PAX2_DOX_TAM_2

data_processing:
Library strategy: GRO-seq
Homer was used to trim polyA tail from 3' end, and only kept sequences longer than 25bp. Command: homerTools Trim -3 AAAAAAAAA -min 25
FastX Toolkit (0.013) was used to filter out low quality reads, (min. 97% of bases should have quality score of 10). Command: fastq_quality_filter -v -q 10 -p 97 -i  input file -o output file
rRNA reads were filtered out with Bowtie 1.1.2. Command: bowtie rRNA_snRNA -q sample --un sample.rRNA_rm > sample.sam
Data was aligned to hg19 assembly with Bowtie 1.1.2. v=2, m=3, k=1.
Homer 4.6 was used to count reads in genes by using analyzeRepeats.pl, both non-adjusted reads and normalized FPKM values were calulated.
Differential expressed genes between treatments were called with DeSeq2 by using Homer command getDiffExpression.pl. -batch option was used to minimize the batch effect between different replicates.
getDistalPeaks.pl command from Homer was used to call intergenic transcripts. Only transcripts has minimu length of 300bp were kept, -intergenic, -noTTS options were used. All Refseq anotated genes (2015/08/31) were exluded.
Homer 4.6 was used to count reads in intergenic transcripts by using analyzeRepeats.pl, both non-adjusted reads and normalized FPKM values were calulated.
Differential expressed intergenic transcripts between treatments were called with DeSeq2 by using Homer command getDiffExpression.pl. -batch option was used to minimize the batch effect between different replicates.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text files include non-normalized read counts and FPKM values for both genes and intergenic transcripts for each sample.

source_name: Mamary gland epithelial cell

growth_protocol: MCF-7 cells were cultured in DMEM with 10% FBS

extract_protocol:
Nuclei were isolated after treatment, then they were used for nuclear run-on reaction (Br-UTP incorporation) followed by RNA isolation with TRIzol LS. Total RNA was used for library preparation.
5 ×10^6 nuclei were used for each run-on reaction, 2 biological replicates were produced for both vehicle and estrogen treatments. Br-UTP was incorporated into on-going transcription by run-on reaction which was performed at 30 degree for 5 min. Total RNA was extracted with TRIzol and fragmented with RNA Fragmentation Reagent. Fragmented RNA was purified with P-30 column, which was followed by T4 polynucleotide kinase treatment to dephosphorylate the 3’ end of RNA fragments. Br-UTP labeled RNA was enriched twice with anti-BrdU beads and precipitated overnight.PolyA tailing was done using E.coli Poly(A) Polymerase, followed by reverse transcription with oNTI-223-index: /5Phos/GATCGTCGGACTGTAGAACTCTGAAC/iSp18/TCAGACGTGTGCTCTTCCGATCTTTTTTTTTTTTTTTTTTTTVN which allows custom barcoding. Exonuclease I was used to remove excess oligo after reverse transcription. DNA-RNA duplex was purified with ChIP DNA Clean & Concentrator Kit followed by RNAse H treatment. cDNA was circularized amplified with oNTI-201: AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACG and oNTI-200: CAAGCAGAAGACGGCATACGAGATXXXXXXGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT(XXXXXX is barcode used for specific sample) for 12 to 14 cycles. Final PCR product was purified by running 10% TBE gel and cleaned up.

treatment_protocol: Cells were treated with doxycycline (50ng/ml) to induce PAX2 oeverexpresson, followed by tamoxifen (1uM) treatment for 6 hours.

value: Breast adenocarcinoma

tag: gender

value: Female

tag: cell line

value: doxycycline + tamoxifen


title: Dox_rep2

description:
analyzeRepeat_PAX2_gene_expression_raw_counts.txt
analyzeRepeat_PAX2_gene_expression_fpkm.txt
analyzeRepeats_PAX2_intergenic_noadj_raw_counts.txt
analyzeRepeats_PAX2_intergenic_fpkm.txt
PAX2_DOX_2

value: doxycycline


title: ChIPseq_IMR90_Input_G

city: Eugene

first: Hideki

last: Tanizawa

state: OR

address: 1370 Franklin Blvd

department: Institute of Molecular Biology

institute: University of Oregon

data_processing:
ChIP-seq: 76-bp or 50-bp reads were aligned to the human genome (hg19) using Bowtie2 (version 2.2.9).
ChIP-seq: Redundant reads were removed by picard (version 2.7.1). Low quality read (MapQ < 10) were also removed.
ChIP-seq peaks were defined by HOMER software (version 4.8.3) using the option “-center -style factor -F 1 -P 0.0001 -fdr 0.05” for RNA Pol II and TP53, while the alternative option “-center -style histone -F 2 -P 0.0001 -fdr 0.05” was used for other proteins. Input samples were used for the control of peak calling.
ChIP-seq score of more than 7-fold compared to the Input were removed from the bigwig file.
Supplementary_files_format_and_content: ChIP-seq: bigwig file were generated using bedGraphToBigWig (version 4)
RNA-seq: Sequenced reads were aligned to the human genome (hg19) using the STAR program (v2.5.2)
RNA-seq: Reads assigned to exons were estimated by the RSEM program (v1.2.31) ), and genes carrying less than 10 reads were eliminated, resulting in total 19,591 genes.
RNA-seq: Read numbers in different samples were normalized using the DEseq2 program ver3.7
RNA-seq: The DEseq2 program was used to identify differently expressed genes. CAP-H2 KD samples (KD#1 and KD#3) were treated as biological replicas. FDR < 0.05 was used as a threshold to identify significantly up- or down-regulated genes.
Supplementary_files_format_and_content: ChIP-seq: bigwig file were generated using bedGraphToBigWig (version 4)
Supplementary_files_format_and_content: RNA-seq: tab-deliminated text files of ensemble gene ID and expected read count obtained from RSEM calculation.

source_name: IMR90 cells

growth_protocol: Normal diploid IMR90 human fibroblasts were cultured in DMEM medium supplemented with 10% FBS, 100 U/ml penicillin, 100 μg/ml streptomycin, 0.15% sodium bicarbonate, 2 mM L-glutamine, 1 mM sodium pyruvate, and 1 ´ MEM non-essential amino acids. BJ human fibroblasts were cultured in DMEM medium supplemented with 10% FBS, 100 U/ml penicillin, and 100 μg/ml streptomycin.

extract_protocol:
In situ Hi-C was performed as previously described (Rao et al., 2014, Cell). ChIP-seq was performed as previously described (Aird et al., 2017 JCB).  RNA was extracted from IMR90 cells using RNeasy Mini kit (Qiagen).  RNA-seq was carried out as previously described with modifications (Tanizawa et al. 2017 NSMB).
For in situ Hi-C, sequencing adapters were ligated using NEBNext Ultra Ligation module (New England Biolabs, Inc) on Dynabeads, and DNA was PCR-amplified for 8-14 cycles using NEBNext Q5 Hot Start HiFi PCR master Mix and NEBNext multiplex oligos (New England Biolabs, Inc). ChIP-seq was carried out as described previously (Iwasaki et al. 2015).  Approximately 1 ng ChIP DNA was subjected to the illumine library construction using NEBNext Ultra DNA library prep kit (New England Biolabs).  Adaptor-ligated DNA was PCR-amplified for 12 cycles using NEBNext Q5 Hot Start HiFi PCR master Mix and NEBNext multiplex oligos (New England Biolabs).  PCR products were sequenced on Illumina NextSeq 500 platform to obtain 76-bp single-end reads.  For RNA-seq, Poly (A) RNA was purified using NEBNext Poly (A) mRNA Magnetic Isolation Module (New England Biolabs), and sequence libraries were constructed using NEBNext mRNA Library prep Master mix for Illumina (New England Biolabs).  Adaptor-ligated DNAs were PCR-amplified for 12 cycles using NEBNext Q5 Hot Start HiFi PCR master Mix and NEBNext multiplex oligos (New England Biolabs).  PCR products were sequenced on Illumina NextSeq 500 platform to obtain 76-bp single-end reads.

treatment_protocol: pBABE-puro plasmids carrying H-rasV12 were used for retrovirus packaging, and virus infection was performed.  H-rasV12-expressing cells were cultured in medium containing 1 µg/ml puromycin for 7 days to obtain OIS cells. pTRIPZ plasmids containing NCAPH2 shRNAs (#1, V3THS_326285; #2, V3THS_326286; #3, V3THS_326290, Dharmacon) were used for CAP-H2 knockdown.  Lentivirus was prepared using ViraPower kit (Thermo Fisher Scientifc) according to the manufacturer’s protocol.  Doxycycline (1μg/ml) was added to culture medium every 48 hours after lentiviral transfection for shRNA expression. OIS cells were further infected with lentivirus encoding one of the three shRNA constructs (#1, #2, and #3) against NCAPH2 and harvested 3 days after the lentivirus infection.

value: Lung fibroblasts

value: wild type

tag: cell status

value: growing cells

tag: passage

tag: karyotype

value: Normal diploid


title: Veh_rep2

description:
analyzeRepeat_PAX2_gene_expression_raw_counts.txt
analyzeRepeat_PAX2_gene_expression_fpkm.txt
analyzeRepeats_PAX2_intergenic_noadj_raw_counts.txt
analyzeRepeats_PAX2_intergenic_fpkm.txt
PAX2_C_2


title: ChIPseq_IMR90_Input_OIS

value: OIS (Oncogene-Induced Senescence) cells


title: Tam_rep2

description:
analyzeRepeat_PAX2_gene_expression_raw_counts.txt
analyzeRepeat_PAX2_gene_expression_fpkm.txt
analyzeRepeats_PAX2_intergenic_noadj_raw_counts.txt
analyzeRepeats_PAX2_intergenic_fpkm.txt
PAX2_TAM_2

value: tamoxifen


title: ChIPseq_IMR90_IgG_G

value: Normal rabbit IgG (Thermo Fisher Scientific, 10500C, lot#503104B)


title: ChIPseq_IMR90_IgG_OIS


title: Veh_rep1

description:
analyzeRepeat_PAX2_gene_expression_raw_counts.txt
analyzeRepeat_PAX2_gene_expression_fpkm.txt
analyzeRepeats_PAX2_intergenic_noadj_raw_counts.txt
analyzeRepeats_PAX2_intergenic_fpkm.txt
PAX2_C_1


title: Tam_rep1

description:
analyzeRepeat_PAX2_gene_expression_raw_counts.txt
analyzeRepeat_PAX2_gene_expression_fpkm.txt
analyzeRepeats_PAX2_intergenic_noadj_raw_counts.txt
analyzeRepeats_PAX2_intergenic_fpkm.txt
PAX2_TAM_1


title: ChIPseq_IMR90_PolII_G

description: Validated by western blot

value: Mouse monoclonal anti-Pol II (Covance, 8WG16, lot# 14944802)


title: Dox_rep1

description:
analyzeRepeat_PAX2_gene_expression_raw_counts.txt
analyzeRepeat_PAX2_gene_expression_fpkm.txt
analyzeRepeats_PAX2_intergenic_noadj_raw_counts.txt
analyzeRepeats_PAX2_intergenic_fpkm.txt
PAX2_DOX_1


title: Arid1a d/d 3

city: Research Triangle Park

first: Ryan

middle: M

last: Marquardt

address: 111 T.W. Alexander Dr, Bldg 101, Room C-416, Mail Drop C-401

department: Reproductive and Developmental Biology Laboratory

institute: National Institute of Environmental Health Sciences

description:
AD3
Gene expression data from uterus at 2 weeks of age.

hyb_protocol: Following fragmentation, 15 ug of aRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array.

scan_protocol: GeneChips were washed and stained in the Affymetrix Fluidics Station 450. GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing:
The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. The normalized, and log transformed intensity values were then analyzed using GeneSpring GX 12.6 (Agilent Technologies, CA).
Fold change filters included the requirement that the genes be present in at least 150% of controls for up-regulated genes and lower than 66% of controls for down-regulated genes. Hierarchical clustering data were clustered groups that behave similarly across experiments using GeneSpring GX 12.6 (Agilent Technologies, CA). Clustering algorithm was Euclidean distance, average linkage.

label: biotin

source_name: uteri of Arid1a d/d at 2 weeks

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Collect uteri from intact 2 week old mice.

extract_protocol: RNA was extracted from the uterine tissues using the RNeasy total RNA isolation kit (Qiagen, Valencia, CA, USA).

value: Arid1a d/d

value: Uterus

tag: Sex

value: 2 weeks


title: Lhx8 P0 Control-2

city: Bethesda

first: Chen-Yu

last: Liu

state: MD

address: 9000, Rockville Pike, Bldg 50, Rm. 3346

institute: NIDDK

data_processing:
removing adapter sequences with cutadapt
aligning the reads with hisat2 against Mus musculus
using featurecounts to estimate the number of gene reads
using a R script to perform differential expression analysis
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: featurecounts output

source_name: Lhx8 P0 Control_ovary

growth_protocol: B6D2F1 mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Ovaries isolated from E18.5 or P0 aged control and knockout mice.

extract_protocol:
Ovaries were isolated, total RNA was isolated using RNeasy Mini Kit and mRNA was purified by Dynabeads mRNA Purification Kit.
Figla RNA-seq library preparation: First strand cDNA was synthesized with SuperScript III Reverse Transcriptase (ThermoFisher Scientific) and the second strand was synthesized in 100 ul containing: 20 ul of the first strand cDNA synthesis mix, 10 ul of 10x second strand buffer (500 mM Tris-HCl, pH 7.5; 50 mM MgCl2; 10 mM DTT), 3 ul of dNTP mix (10 mM), 1 ul of RNase H (2U ul-1), 5 ul of DNA Pol I (10U ul-1) and 61 ul H2O. The mixture was incubated for 2 hr at 16 °C. The libraries were constructed with Nextera DNA Sample Preparation Kit (Illumina) per the manufacturer’s protocol. In summary, double-strand cDNA was fragmented, subjected to adapter ligation and amplified. The RNA-seq library of LHX8 was prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) according to the manufacturer’s instructions.

value: B6D2F1 inbred

value: postnatal day 0

value: ovary


title: Arid1a f/f 3

description:
AF3
Gene expression data from uterus at 2 weeks of age.

source_name: uteri of Arid1a f/f at 2 weeks

value: Arid1a f/f

value: Female


title: Lhx8 P0 Control-3


title: Lhx8 P0 KO-2

source_name: Lhx8 P0 KO_ovary


title: Arid1a d/d 1

description:
AD1
Gene expression data from uterus at 2 weeks of age.


title: Lhx8 P0 KO-1


title: ChIPseq_IMR90_PolII_OIS

description: Validated by western blot


title: Arid1a d/d 2

description:
AD2
Gene expression data from uterus at 2 weeks of age.


title: mESCs_differentiation_control 6h_rep1

source_name: mESC_control 6h_replicate 1

tag: rin

tag: crna yield (microg)

tag: cy3 incorporation (pmol/microg)

tag: time point

value: after 6h treatment

value: vehicle control (DMSO)


title: Arid1a f/f 2

description:
AF2
Gene expression data from uterus at 2 weeks of age.

tag: genotype/variation


title: keratinocyte_Rac1Rac3DKO

city: Kobe

first: Takehiko

last: Ueyama

state: Hyogo

address: Rokkodai-cho 1-1, Nada-ku

department: Biosignal Research Center

institute: Kobe university

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: Total RNA from primary keratinocytes was extracted using NucleoSpin RNA (MACHEREY-NAGEL GmbH & Co. KG).

tag: cell type

value: P3 primary keratinocytes


title: Arid1a f/f 1

description:
AF1
Gene expression data from uterus at 2 weeks of age.


title: keratinocyte_Rac3KO(control)


title: DoxTam_rep1

description:
analyzeRepeat_PAX2_gene_expression_raw_counts.txt
analyzeRepeat_PAX2_gene_expression_fpkm.txt
analyzeRepeats_PAX2_intergenic_noadj_raw_counts.txt
analyzeRepeats_PAX2_intergenic_fpkm.txt
PAX2_DOX_TAM_1

value: Breast adenocarcinoma

tag: agent

value: doxycycline + tamoxifen


title: Lhx8 P0 KO-3

tag: strain

tag: tissue


title: Lhx8 P0 Control-1

tag: age


title: Figla P0 KO-2

source_name: Figla P0 KO_ovary

value: Figla-/-


title: Figla P0 KO-3


title: Figla P0 KO-1


title: Figla P0 Control-3

source_name: Figla P0 Control_ovary

value: Figla+/-


title: Figla E18.5 KO-4

source_name: Figla E18.5 KO_ovary

value: embryonic day 18.5


title: Figla E18.5 KO-3


title: Figla E18.5 Control-4

source_name: Figla E18.5 Control_ovary


title: Figla E18.5 KO-1


title: Figla P0 Control-2


title: Figla E18.5 Control-3


title: Figla E18.5 Control-1


title: N6_EFF

city: Herston

first: Susanna

last: Ng

state: QLD

address: 300 Herston Road

department: Immunology

country: Australia

institute: QIMR Berghofer Medical Research Institute

data_processing:
Sequence reads were trimmed for adapter sequences using Cutadapt (version 1.11) and aligned using STAR (version 2.5.2a)
Sequence reads were aligned to the GRCm38.70.dna.primary assembly with the gene, transcript, and exon features of GRCm38.70 gene model
Quality control metrics were computed using RNA-SeQC (version 1.1.8)
Expression was estimated using RSEM (version 1.2.30)
Genome_build: GRCm38.70.dna.primary
Supplementary_files_format_and_content: tab-seperated values file includes unfiltered, normalised counts per million (cpm)

extract_protocol:
Cells were homogenised in QIAshredder (QIAGEN) columns, followed by RNA extraction using the RNeasy Mini Kit (QIAGEN) according to manufacturer's instructions. Total RNA was treated with the RNase-free DNase Set (QIAGEN).
mRNA was isolated using the NEBNext Poly(A) mRNA magnetic isolation module (New England Biolabs). Libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).

tag: mouse id

value: Th1 cells

value: Spleen

tag: timepoint

value: Day 14 p.i.

tag: infected with

value: Leishmania donovani


title: N4_EFF


title: N6_IL10

value: Treg cells


title: N7_NAIVE

value: Tneg cells


title: N7_IL10


title: N7_TR1

value: Tr1 cells


title: N4_IL10


title: N6_TR1


title: N4_NAIVE


title: N4_TR1


title: N3_EFF


title: N7_EFF


title: N1_EFF


title: N3_IL10


title: Figla E18.5 KO-2

value: B6D2F1 inbred

value: ovary


title: Figla E18.5 Control-2


title: N1_TR1


title: N1_NAIVE


title: N6_NAIVE


title: RNA seq species 2

organism: Chrysopelea ornata

source_name: Cerebellum

value: Cerebellum

value: Adult

tag: genotype

value: Wild-type


title: Pomc+ neuron15

city: Seattle

first: Linda

last: Buck

state: Washington

address: 1100 fairview ave North

department: Basic Sciences

institute: Fred Hutchinson Cancer Research Centre

description:
Manual Isolation
P55

data_processing:
Image analysis and base calling were performed using Illumina real time analysis v1.18 software, followed by 'demultiplexing' of indexed reads and generation of FASTQ files using Illumina's bcl2fastq Conversion software (v1.8.4).
Adapters were trimmed with the “trim_galore” (v.0.4.4, available at http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) with the options “-- adapter AAGCAGTGGTATCAACGCAGAGTAC --stringency 8 --quality 0 -e 0.15 --length 20 --paired --retain_unpaired”.
Sequencing libraries were analyzed with TopHat (v2.1.0) and Cufflinks (v.2.2.1) to generate normalized FPKM values.
Genome_build: mm10 and PRV genome (NC_006151.1)
Supplementary_files_format_and_content: Tab-delimited text files include coordinates of gene annotations, abundance measurements in Fpkm for genes and Fpkm values for signaling molecules considered as positive expression.

source_name: Brain

growth_protocol: For Connect-seq experiments, single cells were FACS sorted into 96 well plates. In manual isolation, cells were manually isolated using micropipette from dissociated mouse brain tissues.

extract_protocol: For Connect-seq experiments,  single cell cDNA libraries were prepared using SMART-seq2 protocol, and for manual isolation, single cell cDNA libraries were prepared using oligo(dT) primed cDNA synthesis followed by PCR amplification of cDNAs (Malnic et al, 1999, Cell, 96:713.  Libraries were prepared for sequencing using the TruSeq DNA sample prep kit (Illumina)

value: Brain


title: Pomc+ neuron13

description:
Manual Isolation
P50


title: Pomc+ neuron14

description:
Manual Isolation
P54


title: Pomc+ neuron12

description:
Manual Isolation
P47


title: Pomc+ neuron11

description:
Manual Isolation
P34


title: Pomc+ neuron8

description:
Manual Isolation
P29


title: N3_NAIVE


title: Pomc+ neuron7

description:
Manual Isolation
P28


title: Pomc+ neuron3

description:
Manual Isolation
P10


title: Pomc+ neuron4

description:
Manual Isolation
P16


title: Pomc+ neuron2

description:
Manual Isolation
P8


title: Pomc+ neuron1

description:
Manual Isolation
A16


title: Pomc+ neuron9

description:
Manual Isolation
P30


title: Pomc+ neuron6

description:
Manual Isolation
P21


title: Pomc+ neuron5

description:
Manual Isolation
P17


title: Unknown111

description:
Connect-seq
Cp27


title: Unknown107

description:
Connect-seq
Cp340


title: Unknown110

description:
Connect-seq
Cp449


title: Unknown106

description:
Connect-seq
Cp339


title: Unknown108

description:
Connect-seq
Cp381


title: N1_IL10


title: Unknown105

description:
Connect-seq
Cp322


title: Unknown103

description:
Connect-seq
Cp301


title: Unknown101

description:
Connect-seq
Cp412


title: Unknown102

description:
Connect-seq
CP_189


title: Pomc+ neuron10

description:
Manual Isolation
P32


title: Unknown100

description:
Connect-seq
Cp315


title: Unknown99

description:
Connect-seq
Cp361


title: Unknown96

description:
Connect-seq
CP_148


title: Figla P0 Control-1

value: postnatal day 0


title: Unknown97

description:
Connect-seq
Cp39


title: Unknown95

description:
Connect-seq
Cp434


title: Unknown109

description:
Connect-seq
Cp384


title: Unknown94

description:
Connect-seq
Cp43


title: N3_TR1


title: Unknown90

description:
Connect-seq
Cp36


title: Unknown91

description:
Connect-seq
Cp463


title: Unknown93

description:
Connect-seq
Cp362


title: Unknown89

description:
Connect-seq
Cp439


title: Unknown87

description:
Connect-seq
Cp32


title: Unknown88

description:
Connect-seq
Cp465


title: Unknown86

description:
Connect-seq
Cp41


title: Unknown85

description:
Connect-seq
Cp472


title: Unknown83

description:
Connect-seq
Cp478


title: Unknown82

description:
Connect-seq
Cp47


title: Unknown84

description:
Connect-seq
Cp84


title: Unknown104

description:
Connect-seq
Cp317


title: Unknown80

description:
Connect-seq
Cp321


title: Unknown81

description:
Connect-seq
Cp48


title: Unknown78

description:
Connect-seq
Cp67


title: Unknown77

description:
Connect-seq
Cp44


title: Unknown75

description:
Connect-seq
CP_188


title: Unknown98

description:
Connect-seq
Cp345


title: Unknown79

description:
Connect-seq
Cp477


title: Unknown76

description:
Connect-seq
Cp312


title: Unknown92

description:
Connect-seq
Cp444


title: Unknown73

description:
Connect-seq
Cp75


title: Unknown72

description:
Connect-seq
Cp382


title: Unknown70

description:
Connect-seq
CP_140


title: Unknown68

description:
Connect-seq
Cp12


title: Unknown67

description:
Connect-seq
CP_192


title: Unknown66

description:
Connect-seq
Cp314


title: Unknown65

description:
Connect-seq
Cp424


title: Unknown64

description:
Connect-seq
Cp50


title: Unknown63

description:
Connect-seq
Cp16


title: Unknown62

description:
Connect-seq
CP_114


title: Unknown59

description:
Connect-seq
Cp354


title: Unknown60

description:
Connect-seq
Cp93


title: Unknown57

description:
Connect-seq
CP_112


title: Unknown58

description:
Connect-seq
Cp40


title: Unknown54

description:
Connect-seq
CP_119


title: Unknown55

description:
Connect-seq
Cp90


title: Unknown53

description:
Connect-seq
Cp294


title: Unknown74

description:
Connect-seq
Cp289


title: Unknown50

description:
Connect-seq
Cp10


title: Unknown49

description:
Connect-seq
Cp83


title: Unknown47

description:
Connect-seq
CP_97


title: Unknown69

description:
Connect-seq
CP_158


title: Unknown48

description:
Connect-seq
CP_174


title: Unknown46

description:
Connect-seq
CP_159


title: Unknown44

description:
Connect-seq
Cp325


title: Unknown45

description:
Connect-seq
Cp383


title: Unknown42

description:
Connect-seq
CP_169


title: Unknown39

description:
Connect-seq
CP_134


title: Unknown61

description:
Connect-seq
Cp396


title: Unknown40

description:
Connect-seq
Cp357


title: Unknown43

description:
Connect-seq
Cp49


title: Unknown38

description:
Connect-seq
Cp452


title: Unknown41

description:
Connect-seq
CP_143


title: Unknown37

description:
Connect-seq
Cp30


title: Unknown36

description:
Connect-seq
CP_170


title: Unknown56

description:
Connect-seq
CP_185


title: Unknown33

description:
Connect-seq
CP_142


title: Unknown35

description:
Connect-seq
Cp328


title: Unknown52

description:
Connect-seq
Cp91


title: Unknown51

description:
Connect-seq
CP_160


title: Unknown31

description:
Connect-seq
Cp20


title: Unknown32

description:
Connect-seq
CP_102


title: Unknown30

description:
Connect-seq
Cp59


title: Unknown28

description:
Connect-seq
Cp292


title: Unknown27

description:
Connect-seq
Cp330


title: Unknown25

description:
Connect-seq
Cp81


title: Unknown26

description:
Connect-seq
Cp52


title: Unknown23

description:
Connect-seq
Cp379


title: Unknown22

description:
Connect-seq
Cp460


title: Unknown20

description:
Connect-seq
Cp74


title: Unknown15

description:
Connect-seq
CP_161


title: Unknown18

description:
Connect-seq
Cp21


title: Unknown16

description:
Connect-seq
Cp372


title: Unknown17

description:
Connect-seq
Cp6


title: Unknown19

description:
Connect-seq
Cp25


title: Unknown12

description:
Connect-seq
Cp355


title: Unknown21

description:
Connect-seq
CP_113


title: Unknown14

description:
Connect-seq
CP_131


title: Unknown9

description:
Connect-seq
Cp457


title: Unknown10

description:
Connect-seq
Cp78


title: Unknown7

description:
Connect-seq
Cp69


title: Unknown13

description:
Connect-seq
Cp394


title: Unknown29

description:
Connect-seq
Cp26


title: Unknown6

description:
Connect-seq
CP_108


title: Unknown24

description:
Connect-seq
Cp298


title: Unknown4

description:
Connect-seq
CP_107


title: Unknown5

description:
Connect-seq
Cp23


title: Unknown1

description:
Connect-seq
Cp326


title: Mixed28

description:
Connect-seq
Cp407


title: Unknown3

description:
Connect-seq
CP_135


title: Unknown2

description:
Connect-seq
CP_141


title: Mixed27

description:
Connect-seq
Cp405


title: Mixed26

description:
Connect-seq
Cp436


title: Mixed25

description:
Connect-seq
CP_184


title: Unknown71

description:
Connect-seq
Cp17


title: Unknown11

description:
Connect-seq
Cp395


title: Mixed21

description:
Connect-seq
Cp352


title: Mixed19

description:
Connect-seq
Cp410


title: Mixed20

description:
Connect-seq
CP_120


title: Mixed16

description:
Connect-seq
Cp429


title: Mixed23

description:
Connect-seq
Cp413


title: Mixed14

description:
Connect-seq
Cp76


title: Mixed15

description:
Connect-seq
Cp409


title: Mixed18

description:
Connect-seq
Cp309


title: Unknown8

description:
Connect-seq
Cp85


title: Mixed13

description:
Connect-seq
Cp387


title: Mixed22

description:
Connect-seq
Cp431


title: Mixed10

description:
Connect-seq
CP_179


title: Mixed17

description:
Connect-seq
CP_149


title: Mixed11

description:
Connect-seq
CP_130


title: Mixed8

description:
Connect-seq
Cp447


title: Mixed6

description:
Connect-seq
Cp60


title: Mixed7

description:
Connect-seq
Cp402


title: Mixed5

description:
Connect-seq
Cp64


title: Mixed9

description:
Connect-seq
Cp401


title: Mixed3

description:
Connect-seq
Cp408


title: Mixed24

description:
Connect-seq
Cp62


title: Oligodendrocyte6

description:
Connect-seq
Cp369


title: Mixed4

description:
Connect-seq
CP_165


title: Oligodendrocyte4

description:
Connect-seq
Cp479


title: Oligodendrocyte2

description:
Connect-seq
Cp79


title: Mixed1

description:
Connect-seq
Cp461


title: Oligodendrocyte1

description:
Connect-seq
Cp58


title: Oligodendrocyte5

description:
Connect-seq
Cp474


title: Mixed12

description:
Connect-seq
CP_167


title: Oligodendrocyte3

description:
Connect-seq
Cp419


title: Microglia29

description:
Connect-seq
Cp480


title: Microglia28

description:
Connect-seq
Cp471


title: Microglia27

description:
Connect-seq
Cp441


title: Microglia30

description:
Connect-seq
Cp467


title: Mixed29

description:
Connect-seq
Cp469


title: Microglia23

description:
Connect-seq
Cp399


title: Microglia24

description:
Connect-seq
Cp470


title: Microglia26

description:
Connect-seq
Cp348


title: Microglia22

description:
Connect-seq
Cp19


title: Mixed2

description:
Connect-seq
Cp392


title: Microglia21

description:
Connect-seq
Cp54


title: Microglia18

description:
Connect-seq
Cp422


title: Microglia19

description:
Connect-seq
Cp18


title: Microglia17

description:
Connect-seq
Cp9


title: Microglia16

description:
Connect-seq
Cp4


title: Microglia15

description:
Connect-seq
Cp414


title: Microglia14

description:
Connect-seq
Cp390


title: Microglia12

description:
Connect-seq
Cp476


title: Microglia13

description:
Connect-seq
Cp473


title: Microglia31

description:
Connect-seq
Cp376


title: Microglia9

description:
Connect-seq
Cp446


title: Microglia11

description:
Connect-seq
Cp57


title: Microglia8

description:
Connect-seq
Cp475


title: Microglia10

description:
Connect-seq
Cp380


title: Microglia7

description:
Connect-seq
Cp45


title: Microglia6

description:
Connect-seq
Cp389


title: Microglia5

description:
Connect-seq
Cp426


title: Microglia25

description:
Connect-seq
Cp458


title: Microglia2

description:
Connect-seq
Cp450


title: Microglia1

description:
Connect-seq
Cp462


title: Microglia4

description:
Connect-seq
Cp459


title: Astrocyte51

description:
Connect-seq
Cp356


title: Microglia3

description:
Connect-seq
Cp453


title: Microglia20

description:
Connect-seq
Cp1


title: Astrocyte52

description:
Connect-seq
Cp428


title: Astrocyte48

description:
Connect-seq
CP_157


title: Astrocyte50

description:
Connect-seq
CP_104


title: Astrocyte47

description:
Connect-seq
CP_124


title: Astrocyte44

description:
Connect-seq
Cp406


title: Astrocyte53

description:
Connect-seq
Cp296


title: Astrocyte43

description:
Connect-seq
CP_162


title: Astrocyte46

description:
Connect-seq
Cp375


title: Astrocyte42

description:
Connect-seq
Cp15


title: Astrocyte45

description:
Connect-seq
Cp393


title: Astrocyte41

description:
Connect-seq
CP_116


title: Astrocyte40

description:
Connect-seq
CP_172


title: Astrocyte38

description:
Connect-seq
Cp14


title: Astrocyte36

description:
Connect-seq
Cp388


title: Astrocyte37

description:
Connect-seq
Cp55


title: Astrocyte39

description:
Connect-seq
Cp427


title: Astrocyte35

description:
Connect-seq
Cp442


title: Astrocyte33

description:
Connect-seq
Cp374


title: Astrocyte34

description:
Connect-seq
Cp366


title: Astrocyte32

description:
Connect-seq
Cp5


title: Astrocyte31

description:
Connect-seq
Cp417


title: Astrocyte49

description:
Connect-seq
Cp344


title: Astrocyte29

description:
Connect-seq
Cp415


title: Astrocyte27

description:
Connect-seq
Cp342


title: Astrocyte28

description:
Connect-seq
CP_147


title: Astrocyte25

description:
Connect-seq
CP_111


title: Astrocyte24

description:
Connect-seq
Cp425


title: Astrocyte23

description:
Connect-seq
CP_118


title: Astrocyte22

description:
Connect-seq
Cp350


title: Astrocyte21

description:
Connect-seq
Cp94


title: Astrocyte18

description:
Connect-seq
Cp404


title: Astrocyte20

description:
Connect-seq
CP_129


title: Astrocyte19

description:
Connect-seq
CP_186


title: Astrocyte16

description:
Connect-seq
CP_100


title: Astrocyte17

description:
Connect-seq
Cp418


title: Astrocyte15

description:
Connect-seq
Cp304


title: Astrocyte14

description:
Connect-seq
Cp297


title: Astrocyte13

description:
Connect-seq
Cp430


title: Astrocyte12

description:
Connect-seq
Cp2


title: Astrocyte11

description:
Connect-seq
Cp385


title: Astrocyte9

description:
Connect-seq
Cp421


title: Astrocyte10

description:
Connect-seq
Cp332


title: Astrocyte7

description:
Connect-seq
Cp360


title: Astrocyte8

description:
Connect-seq
CP_144


title: Astrocyte3

description:
Connect-seq
Cp51


title: Astrocyte4

description:
Connect-seq
CP_106


title: Astrocyte5

description:
Connect-seq
Cp7


title: Astrocyte2

description:
Connect-seq
CP_173


title: Astrocyte6

description:
Connect-seq
Cp82


title: Astrocyte26

description:
Connect-seq
CP_181


title: Astrocyte1

description:
Connect-seq
Cp403


title: Neuron114

description:
Connect-seq
Cp454


title: Neuron115

description:
Connect-seq
CP_133


title: Neuron116

description:
Connect-seq
CP_122


title: Neuron113

description:
Connect-seq
Cp367


title: Neuron112

description:
Connect-seq
Cp464


title: Neuron109

description:
Connect-seq
Cp53


title: Neuron108

description:
Connect-seq
Cp386


title: Neuron111

description:
Connect-seq
Cp468


title: Neuron110

description:
Connect-seq
Cp373


title: Astrocyte30

description:
Connect-seq
CP_150


title: Neuron106

description:
Connect-seq
Cp320


title: Neuron105

description:
Connect-seq
Cp378


title: Neuron103

description:
Connect-seq
Cp35


title: Neuron104

description:
Connect-seq
Cp31


title: Neuron107

description:
Connect-seq
Cp451


title: Neuron100

description:
Connect-seq
Cp364


title: Neuron101

description:
Connect-seq
Cp343


title: Neuron99

description:
Connect-seq
Cp34


title: Neuron117

description:
Connect-seq
Cp334


title: Neuron97

description:
Connect-seq
CP_154


title: Neuron94

description:
Connect-seq
Cp96


title: Neuron96

description:
Connect-seq
Cp435


title: Neuron93

description:
Connect-seq
Cp13


title: Neuron92

description:
Connect-seq
CP_126


title: Neuron95

description:
Connect-seq
Cp33


title: Unknown34

description:
Connect-seq
Cp92


title: Neuron98

description:
Connect-seq
Cp46


title: Neuron89

description:
Connect-seq
CP_155


title: Neuron90

description:
Connect-seq
CP_109


title: Neuron84

description:
Connect-seq
CP_127


title: Neuron86

description:
Connect-seq
Cp295


title: Neuron81

description:
Connect-seq
CP_175


title: Neuron85

description:
Connect-seq
CP_105


title: Neuron87

description:
Connect-seq
Cp22


title: Neuron102

description:
Connect-seq
Cp88


title: Neuron83

description:
Connect-seq
CP_180


title: Neuron91

description:
Connect-seq
Cp11


title: Neuron82

description:
Connect-seq
CP_132


title: Neuron78

description:
Connect-seq
Cp80


title: Neuron79

description:
Connect-seq
CP_121


title: Neuron75

description:
Connect-seq
CP_128


title: Neuron80

description:
Connect-seq
CP_123


title: Neuron88

description:
Connect-seq
Cp86


title: Neuron76

description:
Connect-seq
CP_110


title: Neuron77

description:
Connect-seq
Cp63


title: Neuron74

description:
Connect-seq
Cp398


title: Neuron71

description:
Connect-seq
Cp338


title: Neuron73

description:
Connect-seq
CP_176


title: Neuron72

description:
Connect-seq
Cp443


title: Neuron69

description:
Connect-seq
CP_191


title: Neuron68

description:
Connect-seq
CP_146


title: Neuron67

description:
Connect-seq
Cp411


title: Neuron65

description:
Connect-seq
Cp391


title: Neuron66

description:
Connect-seq
CP_152


title: Neuron62

description:
Connect-seq
Cp437


title: Neuron64

description:
Connect-seq
CP_171


title: Neuron70

description:
Connect-seq
Cp95


title: Neuron57

description:
Connect-seq
CP_99


title: Neuron60

description:
Connect-seq
CP_137


title: Neuron59

description:
Connect-seq
Cp72


title: Neuron61

description:
Connect-seq
CP_164


title: Neuron51

description:
Connect-seq
Cp37


title: Neuron50

description:
Connect-seq
Cp89


title: Neuron53

description:
Connect-seq
CP_166


title: Neuron58

description:
Connect-seq
CP_156


title: Neuron52

description:
Connect-seq
Cp420


title: Neuron49

description:
Connect-seq
Cp363


title: Neuron55

description:
Connect-seq
Cp433


title: Neuron48

description:
Connect-seq
Cp71


title: Neuron47

description:
Connect-seq
CP_178


title: Neuron44

description:
Connect-seq
CP_151


title: Neuron42

description:
Connect-seq
Cp61


title: Neuron45

description:
Connect-seq
Cp42


title: Neuron43

description:
Connect-seq
CP_168


title: Neuron63

description:
Connect-seq
Cp24


title: Neuron41

description:
Connect-seq
Cp87


title: Neuron39

description:
Connect-seq
Cp66


title: Neuron40

description:
Connect-seq
Cp293


title: Neuron38

description:
Connect-seq
Cp68


title: Neuron54

description:
Connect-seq
Cp28


title: Neuron56

description:
Connect-seq
Cp466


title: Neuron46

description:
Connect-seq
CP_190


title: Neuron23

description:
Connect-seq
Cp438


title: Neuron24

description:
Connect-seq
Cp56


title: Neuron34

description:
Connect-seq
Cp65


title: Neuron33

description:
Connect-seq
Cp455


title: Neuron31

description:
Connect-seq
CP_183


title: Neuron26

description:
Connect-seq
CP_98


title: Neuron21

description:
Connect-seq
CP_125


title: Neuron37

description:
Connect-seq
CP_136


title: Neuron18

description:
Connect-seq
CP_101


title: Neuron35

description:
Connect-seq
Cp77


title: Neuron36

description:
Connect-seq
CP_153


title: Neuron19

description:
Connect-seq
Cp400


title: Neuron25

description:
Connect-seq
Cp349


title: Neuron16

description:
Connect-seq
CP_182


title: Neuron27

description:
Connect-seq
CP_145


title: Neuron20

description:
Connect-seq
CP_117


title: Neuron17

description:
Connect-seq
Cp70


title: Neuron15

description:
Connect-seq
Cp423


title: Neuron22

description:
Connect-seq
Cp73


title: Neuron32

description:
Connect-seq
Cp351


title: Neuron30

description:
Connect-seq
CP_138


title: Neuron11

description:
Connect-seq
CP_177


title: Neuron13

description:
Connect-seq
Cp3


title: Neuron28

description:
Connect-seq
CP_163


title: Neuron29

description:
Connect-seq
Cp38


title: Neuron9

description:
Connect-seq
CP_103


title: Neuron10

description:
Connect-seq
Cp29


title: Neuron14

description:
Connect-seq
CP_139


title: Neuron8

description:
Connect-seq
Cp456


title: Neuron7

description:
Connect-seq
Cp316


title: Neuron2

description:
Connect-seq
Cp397


title: Neuron6

description:
Connect-seq
CP_115


title: Neuron1

description:
Connect-seq
CP_187


title: Neuron12

description:
Connect-seq
Cp8


title: Neuron3

description:
Connect-seq
Cp432


title: Neuron5

description:
Connect-seq
Cp448


title: WT-CD4-Stage1_Rep1

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

institute: Monash University

data_processing:
Libraries were mapped to the mm10 genome using Subread-1.6.4, where only uniquely mapped reads were retained. Peaks were called using the findPeaks function in Homer version 4.8.2. Peak-level counts were obtained using featureCounts. Only the peaks that had a CPM (counts per million mapped fragments) value greater than 9 in at least two libraries were used in the downstream analysis.
Counts were converted to log2 CPM, and quantile-normalised with the voom function of the limma package.
A linear model was fitted to each peak and empirical Bayes moderated t-statistic was used to assess differences in expression. Peaks were called differentially accessible (DA) if they achieved a false discovery rate (FDR) less than 0.10.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-CPM values for each library.

source_name: Spleen

extract_protocol:
Cell lysates were treated with Tn5 transposease and DNA was purified following the protocol outlined in Buenrostro et al. 2015 Curr. Protoc. Mol. Biol. 109:21.29.1-9 and Buenrostro et al 2013 Nat. Med. 10(12):1213-8.
Libraries were generated following the following the protocol outlined in Buenrostro et al. 2015 Curr. Protoc. Mol. Biol. 109:21.29.1-9 and Buenrostro et al 2013 Nat. Med. 10(12):1213-8.

treatment_protocol: CD4+ T cells (50,000 cells per replicate) were FACS sorted from mouse spleen and washed with PBS prior to processing for ATAC-seq

tag: celltype

value: CD4+ Foxp3/RFP- CD62L+ IL21/GFP- PD1- CXCR5-

value: Foxp3/RFP x IL21/GFP


title: Naïve-Tregs_Rep3

value: CD4+ Foxp3/RFP+ CD62L+ IL21/GFP- PD1- CXCR5-


title: WT-CD4-Stage1_Rep2


title: Neuron4

description:
Connect-seq
Cp445


title: Naïve-Tregs_Rep2


title: Activated-CD4_Rep3

value: CD4+ Foxp3/RFP- CD62L- IL21/GFP- PD1- CXCR5-


title: Activated-CD4_Rep4

value: Spleen


title: Activated-Tregs_Rep2

value: CD4+ Foxp3/RFP+ CD62L- IL21/GFP- PD1- CXCR5-


title: Activated-Tregs_Rep1


title: Activated-CD4_Rep2


title: Late passage of MEF cells derived from Wild-type mice replicat 1

city: Lyon

first: jean-michel

last: flaman

address: 28 rue Laennec

department: CRCL

country: France

institute: Inserm 1052

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. After fragmentation 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent GE Whole Human Genome Oligo Microarrays (Agilent-026652) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried briefly in acetonitrile.

scan_protocol: Microarrays were scanned with an Agilent DNA microarray scanner G2565CA (Agilent Technologies).Fluorescent signals were extracted and normalized with the Feature Extraction software version 10.5.1.1 (Agilent Technologies),

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.3.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Late passage Wild-type MEFs

label_protocol: cRNAs were synthesized and labeled with the Cy3 dye from 100 ng of total RNA using the one-color Low Input Quick Amp Labeling Kit (Agilent Technologies) following the manufacturer's recommandations, followed by RNeasy Mini column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Mouse Embryonic Fibroblasts (MEFs) were prepared with embryos at E12.5 and cultured in Dulbecco′s modified Eagle′s medium with GlutaMax, 10% FBS, 1% penicillin/streptomycin and 1% of Gibco™ MEM Non-Essential Amino Acids Solution (ThermoFisher Scientific).

extract_protocol: Total RNA was extracted from MEFs in culture using Nucleospin RNA kit (Macherey Nagel)

treatment_protocol: MEFs were cultured during 3 passages (Early passage) or 5 passages (Late passage)

tag: passage

value: Late


title: Late passage of MEF cells derived from Itpr2 Knock-out mice replicat 1

source_name: Late passage Itpr2 KO MEFs

value: Itpr2 KO


title: Late passage of MEF cells derived from Itpr2 Knock-out mice replicat 3


title: Early passage of MEF cells derived from Wild-type mice replicat 3

source_name: Early passage Wild-type MEFs

value: Early


title: Early passage of MEF cells derived from Itpr2 Knock-out mice replicat 1

source_name: Early passage Itpr2 KO MEFs


title: Itpr2KO mouse liver replicate 1

source_name: liver

growth_protocol: C57Bl/6 wild-type and Itpr2 KO mice were maintained in laminar-flow boxes under standard conditions (standard diet and water) in a specific pathogen-free animal facility. At 23 month old mice were sacrificed and livers were removed and snap-frozen

extract_protocol: Total RNA was extracted from frozen livers after a step of cryogrinding using Nucleospin RNA kit (Macherey Nagel)

treatment_protocol: No specific treatment - Survival cohort

value: Itpr2 Knock-out


title: Late passage of MEF cells derived from Wild-type mice replicat 2


title: Itpr2KO mouse liver replicate 3


title: Late passage of MEF cells derived from Itpr2 Knock-out mice replicat 2

source_name: Late passage Itpr2 KOMEFs


title: Late passage of MEF cells derived from Wild-type mice replicat 3


title: Early passage of MEF cells derived from Wild-type mice replicat 2


title: Early passage of MEF cells derived from Itpr2 Knock-out mice replicat 2


title: Itpr2KO mouse liver replicate 2


title: Wild-type mouse liver replicate 3


title: Early passage of MEF cells derived from Itpr2 Knock-out mice replicat 3


title: Early passage of MEF cells derived from Wild-type mice replicat 1


title: Wild-type mouse liver replicate 1


title: Naïve-Tregs_Rep1


title: Bach2 Deficiency Rep2

data_processing:
Libraries were mapped to the mm10 genome using Subread-1.6.4, where only uniquely mapped reads were retained. Genewise counts were obtained using featureCounts. Only the genes that had a CPM (counts per million mapped fragments) value greater than 0.5 in at least two libraries were used in the downstream analysis.
Counts were converted to log2 CPM, and quantile-normalised with the voom function of the limma package. Log2 CPM values were then converted to log2 FPKM values.
A linear model was fitted to each gene and empirical Bayes moderated t-statistic was used to assess differences in expression. Genes were called differentially expressed (DE) if they achieved a false discovery rate (FDR) less than 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file 'Supp_Raw_Counts.txt' includes raw read counts for genes in each library.

extract_protocol:
RNA purification was performed following the manufacturer’s protocol using the RNeasy Plus Mini Kit (Qiagen).
mRNA reverse transcription and cDNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

treatment_protocol: CD4+ T cells (30,000 cells per replicate) were FACS sorted from mouse spleen, washed with PBS and lysed immediately prior to RNA extraction.

value: CD4+ Foxp3+ Treg cell


title: Cre Rep2


title: Cre Rep1


title: Activated-CD4_Rep1


title: Wild-type mouse liver replicate 2


title: 72h-IRF4-rep1

data_processing:
Libraries were mapped to the mm10 genome using Subread-1.6.0, and only uniquely mapped reads were retained. Genewise counts were obtained using featureCounts. Only the genes that had a CPM (counts per million mapped fragments) value greater than 0.5 in at least one library and had official symbols were used in the downstream analysis.
Counts were converted to log2 CPM, quantile-normalized, and precision-weighted with the voom function of the limma package. Log2 CPM values were then converted to log2 FPKM values.
A linear model was fitted to each gene and empirical Bayes moderated t-statistic was used to assess differences in expression. Genes were called differentially expressed (DE) if they achieved a false discovery rate (FDR) of <0.05. A minimum fold change of 2 between the two conditions was then required for calling the DE genes from each of the comparisons.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized log2-FPKM values for each library. The supplementary file, 'RNA_Supp_Raw_Counts.txt', includes raw read counts for genes in each library (before CPM filtering).

source_name: spleens and lymph nodes

growth_protocol: CD4+ T cells (30,000 cells per replicate) were FACS sorted from mouse spleen and lymph node, and cultured in complete IMDM supplemented with 100 U/ml recombinant human IL-2, 0.5 ng/ml TGFb, 10 ug/ml anti-IL4 antibody, 10 ug/ml anti-IFNg antibody, 2ug/ml anti-CD28 antibody, and with 10 ug/ml plate-bound anti-CD3 antibody.

treatment_protocol: Cells were washed twice with PBS prior to RNA extraction.

value: CD4+ T cells

tag: time

value: 72 hours


title: 72h-Bach2-rep1

value: Bach2 -/-


title: 72h-WT-rep2

value: Wildtype


title: 24h-WT-rep1

value: 24 hours


title: 72h-WT-rep1


title: 24h-WT-rep2


title: 72h-IRF4-rep2


title: 72h-Bach2-rep2


title: 24h-IRF4-rep1


title: 72h-DKO-rep2


title: 24h-Bach2-rep2


title: 24h-DKO-rep1


title: 0h-WT-rep2

value: 0 hour


title: 24h-Bach2-rep1


title: 0h-WT-rep1


title: 0h-Bach2-rep2


title: 24h-DKO-rep2


title: 0h-Bach2-rep1


title: 0h-DKO-norep


title: 0h-IRF4-rep1


title: 72h-DKO-rep1


title: IRF4-B-72h

data_processing:
The samples were mapped to the mm10 genome using Subread-1.6.0, and only uniquely mapped reads were retained. Peaks were called on the mapping results of the two samples belonging to each sample type (as replicates) by using Homer-4.7 at false-discovery rate cutoffs (FDR) of 0.05 for the 0h samples, and 1E-10 for the 72h samples.
The peaks from all the sample types were merged into non-overlapping regions by taking unions of them, and the counts of read-pairs in the individual samples falling into the merged regions were obtained using featureCounts. Only the regions that had a CPM (counts per million mapped fragments) value greater than 8 in at least two samples were used in the downstream analysis.
Counts were converted to log2 CPM, quantile-normalized, and precision-weighted with the voom function of the limma package.
A linear model was fitted to each region and empirical Bayes moderated t-statistic was used to assess differences in accessibility. Regions were called differentially accessible (DA) if they achieved a FDR of less than 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: TAB-delimited text files include normalized log2-CPM values in each library. The supplementary file, ATAC_Supp_Raw_Counts.txt, includes raw read-pair counts for merged peaks in each library (before CPM filtering).

value: CD4 T cells


title: WT-A-72h


title: IRF4-B-0h


title: WT-B-0h


title: 24h-IRF4-rep2


title: 0h-IRF4-rep2


title: IRF4-A-72h


title: Bach2-B-0h


title: Bach2-A-72h


title: IRF4-A-0h


title: Bach2-A-0h


title: Bach2-B-72h


title: Irf4ChIP-Bach2KO-rep2

data_processing:
The samples were mapped to the mm10 genome using Subread-1.6.0, and only uniquely mapped reads were retained. Peaks were called on the mapping results using Homer-4.7: (1) Irf4ChIP-Bach2KO-rep1 and Irf4ChIP-Bach2KO-rep2 against Irf4ChIP-Bach2KO-Input-rep1 and Irf4ChIP-Input-rep2 ; (2) Irf4ChIP-WT-rep1 and Irf4ChIP-WT-rep2 against Irf4ChIP-WT-Input-rep1 and Irf4ChIP-Input-rep2 ; (3) Bach2ChIP-WT-rep1 and Bach2ChIP-WT-rep2 with no input samples. A false-discovery rate cutoff (FDR) of 1E-3 was used on the Bach2-ChIP samples, and 1E-8 was used on the Irf4-ChIP samples.
The peaks called from the Irf4-ChIP samples were then filtered by their Fragments Per Kilobase of peak region per Million (FPKM) values in the ChIP samples and the input samples. A peak was kept in the analysis only if it has a minimum FPKM of 2 in the ChIP samples where it was called, and also has a maximum FPKM of 2 in the corresponding input samples. A minimum Fold Change (FC) of 5 was also required between the minimum FPKM value in the ChIP samples and the maximum FPKM value in the corresponding input samples. These FPKM and FC filters were not applied on the peaks called from the Bach2-ChIP samples. The lists of peaks were then submitted to this repository as "processed data files".
Please be aware that the peak lists submitted to this repository were not filtered using the peaks called from our ATAC-seq samples, however the ChIP-seq peaks finally used in the paper were filtered by requiring at least one base overlapping with any ATAC-seq peak. Please find the details in the paper.
Genome_build: mm10
Supplementary_files_format_and_content: Three supplementary files: Bach2ChIP-WT-Q1e-3-Before-ATACseq-Fltr.txt, Irf4ChIP-Bach2KO-Q1e-8-Before-ATACseq-Fltr.txt and Irf4ChIP-WT-Q1e-8-Before-ATACseq-Fltr.txt are the lists of peaks called by Homer, after RPKM and FC filtering (for the two Irf4-ChIP peak lists), but before ATAC-seq peak filtering.

growth_protocol: CD4+ T cells (10,000,000 cells per replicate) were FACS sorted from mouse spleen and lymph node, and cultured in complete IMDM supplemented with 100 U/ml recombinant human IL-2, 0.5 ng/ml TGFb, 10 ug/ml anti-IL4 antibody, 10 ug/ml anti-IFNg antibody, 2ug/ml anti-CD28 antibody, and with 10 ug/ml plate-bound anti-CD3 antibody.

extract_protocol: DNA libraries were prepared using the TruSeq RNA Sample preparation kit (Illumina) following the manufacturer’s instructions.

tag: chip antibody


title: WT-A-0h


title: Bach2ChIP-WT-rep1


title: Irf4ChIP-Bach2KO-Input-rep1

value: input sample


title: Irf4ChIP-Input-rep2


title: Bach2 Deficiency Rep1


title: Irf4ChIP-WT-rep1


title: HPFcells treated with hypoxia replicate 2

city: Stillwater

first: CHAOQUN

last: HUANG

state: OK

address: 264 McElroy Hall

department: Physiological Sciences

institute: Oklahoma State University

description: Hypoxia Control2

data_processing:
The indexed libraries were pooled in equal molar ratio and sequenced on the Illumina NextSeq 500 system using 2x75bp paired-end sequencing.
Paired-end reads were directionally mapped to the genomic loci of lncRNA and mRNA (GRCh37 /hg19) by TopHat2.
Cufflinks/Cuffdiff analysis was run to identify the dysregulated RNAs
Genome_build: GRCh37 /hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values generated by cufflinks

source_name: HPF fibroblast cells

extract_protocol:
Total RNA was isolated from HPF cells  by using Tri Reagents
Libraries were prepared with the Illumina TruSeq Stranded mRNA Library Preparation kit. Briefly, poly-adenylated mRNA were selected using oligo-dT beads and fragmented to 300-500bp. Each fragment undergoes cDNA synthesis using random hexamer. Indexed adapters were ligated to the resulting cDNA.

value: Lung

value: Fibroblast

tag: Sex

value: male


title: HPFcells treated with hypoxia and TGFβ1 replicate 2

description: Hypoxia TGFβ1-2


title: HPFcells treated with hypoxia replicate 3

description: Hypoxia Control3


title: HPFcells treated with hypoxia and TGFβ1 replicate 3

description: Hypoxia TGFβ1-3


title: HPFcells treated with hypoxia replicate 1

description: Hypoxia Control1


title: HPFcells treated with TGFβ1 replicate 3

description: Normoxia TGFβ1-3


title: HPFcells treated with TGFβ1 replicate 2

description: Normoxia TGFβ1-2


title: HPFcells treated with PBS replicate 3

description: Normoxia Control3


title: HPFcells treated with PBS replicate 2

description: Normoxia Control2


title: Irf4ChIP-WT-rep2


title: WT-B-72h


title: HPFcells treated with PBS replicate 1

description: Normoxia Control1


title: HPFcells treated with hypoxia and TGFβ1 replicate 1

description: Hypoxia TGFβ1-1


title: Irf4ChIP-WT-Input-rep1


title: Bach2ChIP-WT-rep2


title: LSD1_Input_ChIPSeq

city: Boston

first: Robert

last: Policastro

state: Massachusetts

address: 451 D St Unit #600

institute: Ensoma Inc.

data_processing:
Quality of sequencing reads assessed with FastQC (v0.11.5).
Reads were aligned to the hg38 genome using Bowtie2 (v2.3.2) with additional parameters -q --phred33 --sensitive --end-to-end --no-unal --no-mixed --no-discordant. The Bowtie2 genome index used for alignment was downloaded from Illumina iGenomes on Sun Jan 27 02:01:22 EST 2019.
SAM files were coordinate sorted and indexed using Samtools (v1.9).
Peaks were called using MACS (v2.1.0) with the appropriate input or KO controls, with additional parameters -g hs -q 0.05
Bedtools (v2.26.0) was used to find intersecting peaks between replicates.
bigWigs were created using deepTools (v3.1.3) bamCoverage with additional parameters -bs 1 --normalizeUsing CPM and --extendReads 150 for single end, or --extendReads for paired end samples.
Genome_build: hg38
Supplementary_files_format_and_content: bed
Supplementary_files_format_and_content: bigwig

source_name: SW480 Cells

extract_protocol:
Cells were trypsonized prior to histone ChIP-seq (iDeal ChIP-seq Kit for Histones, Diagenode: C01010051) or scraped prior to transcription factor ChIP-seq (iDeal ChIP-seq kit for Transcription Factors, Diagenode: C01010055).
Libraries were generated for sequencing using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) per manufacturer’s protocol.

value: wildtype

value: none, input


title: LSD1_R2_ChIPSeq

value: LSD1 (abcam, ab17721)


title: H3K4me2_Input_KD_ChIPSeq

value: LSD1 knockdown


title: HPFcells treated with TGFβ1 replicate 1

description: Normoxia TGFβ1-1


title: H3K4me2_Input_EV_ChIPSeq

value: empty vector


title: Irf4ChIP-Bach2KO-rep1


title: LSD1_R1_ChIPSeq


title: H3K4me2_KDR3_ChIPSeq

description:
LSD1 knockdown replicate 3
K4me2-merge_KD_intersect.bed


title: H3K4me2_EVR2_ChIPSeq

description:
empty vector replicate 2
K4me2-merge_EV_intersect.bed


title: H3K4me2_KDR2_ChIPSeq

description:
LSD1 knockdown replicate 2
K4me2-merge_KD_intersect.bed


title: SW480_GSKLSD1R2_RNASeq

description:
GSK-LSD1 replicate 2 (Not Stranded)
SW480-GSKLSD1_raw_counts.txt

data_processing:
Quality of sequencing reads assessed with FastQC (v0.11.5).
An index of the hg38 genome was created, and reads were aligned with STAR (v2.6.1a) with the additional parameter --outSAMtype BAM SortedByCoordinate.
Coordinated sorted BAM files were indexed with Samtools (v1.9).
Reads were assigned to the nearest gene and counted using Rsubread (v1.24.2) with the additional parameters: isGTFAnnotationFile=TRUE GTF.featureType='exon' GTF.attrType='gene_id' useMetaFeatures=TRUE allowMultiOverlap=FALSE minOverlap=5 countMultiMappingReads=TRUE isPairedEnd=FALSE and either strandSpecific=2 or strandSpecific=0 depending on whether the library preparation was strand specific or not.
EdgeR (v3.24.0) was used for differential expression analysis. Genes with CPM expression less than 0.5 in more than one sample replicate were excluded from the model.
Genome_build: hg38
Supplementary_files_format_and_content: raw_counts

extract_protocol:
Cells were collected by scraping prior to total RNA isolation using RNeasy mini kit (Qiagen, 74104).
Libraries were generated using Illumina TruSeq Stranded mRNA (Illumina, 20020594).


title: SW480_DMSOR2_RNASeq

description:
DMSO replicate 2 (Not Stranded)
SW480-GSKLSD1_raw_counts.txt

value: DMSO


title: SW480_GSKLSD1R3_RNASeq

description:
GSK-LSD1 replicate 3 (Not Stranded)
SW480-GSKLSD1_raw_counts.txt


title: SW480_GSKLSD1R1_RNASeq

description:
GSK-LSD1 replicate 1 (Not Stranded)
SW480-GSKLSD1_raw_counts.txt


title: H3K4me2_KDR1_ChIPSeq

description:
LSD1 knockdown replicate 1
K4me2-merge_KD_intersect.bed


title: HT29_KDR3_RNASeq

description:
LSD1 knockdown replicate 3 (Stranded)
HT29-KD_raw_counts.txt

source_name: HT29 Cells


title: SW480_DMSOR1_RNASeq

description:
DMSO replicate 1 (Not Stranded)
SW480-GSKLSD1_raw_counts.txt


title: SW480_DMSOR3_RNASeq

description:
DMSO replicate 3 (Not Stranded)
SW480-GSKLSD1_raw_counts.txt


title: H3K4me2_EVR1_ChIPSeq

description:
empty vector replicate 1
K4me2-merge_EV_intersect.bed


title: HT29_KDR1_RNASeq

description:
LSD1 knockdown replicate 1 (Stranded)
HT29-KD_raw_counts.txt


title: HT29_EVR2_RNASeq

description:
empty vector replicate 2 (Stranded)
HT29-KD_raw_counts.txt


title: HT29_EVR3_RNASeq

description:
empty vector replicate 3 (Stranded)
HT29-KD_raw_counts.txt


title: LSD1_LSD1KO_ChIPSeq

value: LSD1 knockout


title: HT29_KDR2_RNASeq

description:
LSD1 knockdown replicate 2 (Stranded)
HT29-KD_raw_counts.txt


title: SW480_KDR3_RNASeq

description:
LSD1 knockdown replicate 3 (Stranded)
SW480-KD_raw_counts.txt


title: HT29_EVR1_RNASeq

description:
empty vector replicate 1 (Stranded)
HT29-KD_raw_counts.txt


title: SW480_KDR2_RNASeq

description:
LSD1 knockdown replicate 2 (Stranded)
SW480-KD_raw_counts.txt


title: SW480_KDR1_RNASeq

description:
LSD1 knockdown replicate 1 (Stranded)
SW480-KD_raw_counts.txt


title: Clone10GFPpos_3

city: New York

first: Kelly

middle: Madigan

last: Banks

state: NY

address: 1300 York Ave, LC711

department: Surgery

institute: Weill Cornell Medicine

description: RNA seq

data_processing:
Raw reads were aligned using STAR v2.3.0e_r291
Read counting was performed using htseq-count v0.6.0
Differential gene expression analysis using DeSeq2
Gene enrichment analysis using GSEA
Genome_build: mm10
Supplementary_files_format_and_content: raw counts
Supplementary_files_format_and_content: DeSeq results

source_name: mESC

growth_protocol: mESCs were cultured in KO DMEM, 1% GlutaMAX, 1x Pen-Strep. 1x NEAA, 0.1 mM 2-Mercaptoethanol, 1000 units/ml rmLIF, and 15% Serum

extract_protocol:
RNA was extracted using Qiagen RNeasy kit
Libraries prepared using IlluminaTruSeq RNA Sample Preparation Kits v2

treatment_protocol: 6 uM (Z)-4-Hydroxytamoxifen for 48 hours

value: GFP+ Sphk1-/- Sphk2-/-


title: SW480_EVR3_RNASeq

description:
empty vector replicate 3 (Stranded)
SW480-KD_raw_counts.txt


title: Clone10GFPneg_3

description: RNA seq

value: GFP- Sphk1fl/fl Sphk2-/-


title: H3K4me2_EVR3_ChIPSeq

description:
empty vector replicate 3
K4me2-merge_EV_intersect.bed


title: SW480_EVR1_RNASeq

description:
empty vector replicate 1 (Stranded)
SW480-KD_raw_counts.txt


title: Clone10GFPpos_2

description: RNA seq


title: Clone10GFPneg_2

description: RNA seq


title: Clone4GFPpos_2

description: RNA seq


title: Clone4GFPneg_3

description: RNA seq


title: Clone4GFPneg_2

description: RNA seq


title: Clone4GFPpos_3

description: RNA seq


title: Clone10GFPpos_1

description: RNA seq


title: Clone4GFPneg_1

description: RNA seq